No. of threads for alignment

[dena.dinesh]

Hi,

I have desktop with following configurations:

RAM:128GB
OS:Ubuntu
CPUs:40
On-line CPU(s) list:0-39
Thread(s) per core:2
Core(s) per socket:10

So If want to do alignment using bowtie or tophat, what is the maximum numebr of threads can specified for parameter "p" to facilititate faster mapping of reads.

If I want to run mapping parallely for multiple fastq files, how many number of threads can I specify to make alignment faster.

[GenoMax]

Unless you have a high speed disk sub-system at some point the processes may become I/O bound. You will need to experiment with what works on your rig (start with a sub-sampled dataset, say 50000 reads and 8 or 12 threads). Work your way up or down based on results.